However, MetService forecaster Andy Downs said there was potential for more squally thunderstorms along Waikato's west coast tomorrow.

"It could be squally with very strong winds and there's still a slight risk of these ones we get tomorrow afternoon of small tornadoes but I don't think on the same scale of the one we saw in Auckland, so I don't want to get people panicked about that."

A tornado hit near Rotorua this afternoon after an earlier twister smashed west Auckland, killing three people, injuring seven and leaving hundreds homeless.

The Auckland tornado, which struck about 12.15pm today, ripped roofs from houses, toppled trees and sent debris flying. It was followed three hours later by a second, smaller, tornado near Rotorua.

Fire Service spokesman Colin Underdown said firefighters were called to the Hamurana area, on the northern shore of Lake Rotorua, about 3.20pm after a small tornado touched down.

Forty children and 13 adults from a Mokoia Intermediate School group were horse riding in the area, about 20km north of Rotorua when the tornado struck.

Rotorua District Council emergency management coordinator Pauline Hitchcock confirmed all school group were safe and well. It was earlier reported that one child was understood to have been injured.

Mokoia Intermediate principal Deborah Epp said when the "mini tornado" occurred the children got off their horses and found shelter in a nearby building.

MetService meteorologist Daniel Corbett said tomorrow would be showery and there would be gusty, gale-force winds on Waikato's west coast.

Nearly 250 residents whose homes have been made uninhabitable were given shelter at the Whenuapai Air Force base.

Hobsonville Point residents have been ordered to take shelter in their homes with the MetService warning of the potential for further tornadoes. Police set up an operational base at the worst-hit Whenuapai.

Ambulance staff reported two deaths from the storm at a school construction site off Hobsonville Rd. A third death was later confirmed.

Hobsonville Point Primary School principal Daniel Birch said two construction workers were killed at the site where a secondary school was being built.

"There's two schools being built, the primary school site which wasn't in the path of the tornado and the secondary school site where the two workers were killed."

The residential centre of the tornado's destruction was Wallingford Way, in Hobsonville; a street lined with Defence Force state housing.

Every house in Wallingford Way has been damaged. Windows are broken, roofs damaged and trees uprooted.

Most residents have been evacuated from the street. The army and emergency services were working to clear debris.

A resident said they saw wheelie bins and pot plants flying past their windows and were forced to duck for shelter as windows smashed in. Urban Search and Rescue (Usar) members, already in the area for training, have been diverted to check houses.

Andy Gummer from St John Amulance said so far seven people had been transported to North Shore hospital with minor and moderate injuries.